I still think it’s worth a call to Steinberg regarding the MR. I use S/PDIF into a MOTU for (stereo) headphone monitoring, but I can still route the S/PDIF from the MOTU to two seperate mono busses and from there to the inputs of two seperate mono tracks. The MOTU is locked by workclock though … not an option on the Alpha?
[EDIT] Just did a little bit of research: it turns out it is the MR816X after all:
SPDIF and Direct monitoring
… so until they fix this, yes, you’ll have to record in stereo if you want to use direct monitoring and split the file using one of the techniques described above! Apologies if I didn’t quite get what you were describing initially.